Is there a way to bake a model's normal map in chunks?
If you uncheck Clear Image checkbox in the Bake/Output you will be able to bake from different chunks sequently to the same image. You may want to lower the Margin distance so that the margin wont overwrite previous bakes.

Another way of dealing with this type of problems is to (copy and) move different parts together with their high-poly counterparts so they will be baked all at ones but without intersecting with each other.

Or, as previous suggested, create a cage mesh so you can control the ray length in detail.